Protein Structure Analysis with Constraint Programming.

Abstract

In this chapter, we present a review of various approaches to modeling protein structure by means of constraint programming. This particular programming framework has been used in the modeling of the structure and properties of chemical compounds. Even though not as widespread as other approaches (e.g., those based on physical and chemical simulations), this methodology offers several advantages in terms of declarative modeling and search of solutions. For example, it is possible (1) to describe the position and mobility of objects through constraints, (2) to employ reasoning techniques to reduce the set of potential solutions and (3) to use energetic or cost constraints in order to formulate an optimization problem. After a brief introduction to constraint programming and some notes about its use with molecular structures, we present various applications ranging from proof of concepts to working packages (see, e.g., PSICO2) based on this technology.